Mtd-energy: Difference between revisions
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Navigation: [[Documentation]] / [[Methods]] / [[Metadynamics]] / [[MTD:Utilities]] / [[mtd-energy]] | Navigation: [[Documentation]] / [[Methods]] / [[Metadynamics]] / [[MTD:Utilities]] / [[mtd-energy]] | ||
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'''Synopsis''' | '''Synopsis''' | ||
<span style="color: maroon;">mtd-energy</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">input | <span style="color: maroon;">mtd-energy</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">input output </span> | ||
'''Description''' | '''Description''' | ||
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{| style="margin-left: 2em; width: 95%;" | {| style="margin-left: 2em; width: 95%;" | ||
|- style="vertical-align: top; background-color: #e6e6e6;" | |- style="vertical-align: top; background-color: #e6e6e6;" | ||
|<span style="color: blue;">-t, --time NUMBER</span><br/><span style="margin-left: 30px;">Specifies metadynamics time that will be used for the energy calculation.</span><br/><span style="color:purple; margin-left: 30px;">(Default: 0)</span> | |<span style="color: blue;">-t, --time NUMBER</span><br/><span style="margin-left: 30px;">Specifies metadynamics time that will be used for the energy calculation.</span><br/><span style="color:purple; margin-left: 30px;"> (Default: 0)</span> | ||
|- style="vertical-align: top;" | |- style="vertical-align: top; " | ||
|<span style="color: blue;">--offset REAL</span><br/><span style="margin-left: 30px;">Determine position of global minima.</span><br/><span style="color:purple; margin-left: 30px;">(Default: 0)</span> | |<span style="color: blue;">--offset REAL</span><br/><span style="margin-left: 30px;">Determine position of global minima.</span><br/><span style="color:purple; margin-left: 30px;"> (Default: 0)</span> | ||
|- style="vertical-align: top; background-color: #e6e6e6;" | |- style="vertical-align: top; background-color: #e6e6e6;" | ||
|<span style="color: blue;">--smooth NUMBER</span><br/><span style="margin-left: 30px;">Calculate the energy surface average from time interval SMOOTH to TIME.</span><br/><span style="color:purple; margin-left: 30px;">(Default: 0)</span> | |<span style="color: blue;">--smooth NUMBER</span><br/><span style="margin-left: 30px;">Calculate the energy surface average from time interval SMOOTH to TIME.</span><br/><span style="color:purple; margin-left: 30px;"> (Default: 0)</span> | ||
|- style="vertical-align: top;" | |- style="vertical-align: top; " | ||
|<span style="color: blue;">--sd</span><br/><span style="margin-left: 30px;">Print the standard deviation of the free energy when the smoothing is enabled.</span> | |<span style="color: blue;">--sd</span><br/><span style="margin-left: 30px;">Print the standard deviation of the free energy when the smoothing is enabled.</span> | ||
|- style="vertical-align: top; background-color: #e6e6e6;" | |- style="vertical-align: top; background-color: #e6e6e6;" | ||
|<span style="color: blue;">--output FORMAT</span><br/><span style="margin-left: 30px;">Output FORMAT, which will be used to print free energy surface. Supported formats are: plain, gnuplot, fes.</span><br/><span style="color:purple; margin-left: 30px;">(Default: gnuplot)</span> | |<span style="color: blue;">--output FORMAT</span><br/><span style="margin-left: 30px;">Output FORMAT, which will be used to print free energy surface. Supported formats are: plain, gnuplot, fes.</span><br/><span style="color:purple; margin-left: 30px;"> (Default: gnuplot)</span> | ||
|- style="vertical-align: top;" | |- style="vertical-align: top; " | ||
|<span style="color: blue;">--noheader</span><br/><span style="margin-left: 30px;">Do not print header to output file.</span> | |<span style="color: blue;">--noheader</span><br/><span style="margin-left: 30px;">Do not print header to output file.</span> | ||
|- style="vertical-align: top; background-color: #e6e6e6;" | |- style="vertical-align: top; background-color: #e6e6e6;" | ||
|<span style="color: blue;">--fx FORMAT</span><br/><span style="margin-left: 30px;">Output FORMAT, which will be used to print values of collective variables.</span><br/><span style="color:purple; margin-left: 30px;">(Default: %15.7le)</span> | |<span style="color: blue;">--fx FORMAT</span><br/><span style="margin-left: 30px;">Output FORMAT, which will be used to print values of collective variables.</span><br/><span style="color:purple; margin-left: 30px;"> (Default: %15.7le)</span> | ||
|- style="vertical-align: top;" | |- style="vertical-align: top; " | ||
|<span style="color: blue;">--fe FORMAT</span><br/><span style="margin-left: 30px;">Output FORMAT, which will be used to print values of free energy.</span><br/><span style="color:purple; margin-left: 30px;">(Default: %15.7le)</span> | |<span style="color: blue;">--fe FORMAT</span><br/><span style="margin-left: 30px;">Output FORMAT, which will be used to print values of free energy.</span><br/><span style="color:purple; margin-left: 30px;"> (Default: %15.7le)</span> | ||
|- style="vertical-align: top; background-color: #e6e6e6;" | |- style="vertical-align: top; background-color: #e6e6e6;" | ||
|<span style="color: blue;">--fs FORMAT</span><br/><span style="margin-left: 30px;">Output FORMAT, which will be used to print values of standard deviations.</span><br/><span style="color:purple; margin-left: 30px;">(Default: %15.7le)</span> | |<span style="color: blue;">--fs FORMAT</span><br/><span style="margin-left: 30px;">Output FORMAT, which will be used to print values of standard deviations.</span><br/><span style="color:purple; margin-left: 30px;"> (Default: %15.7le)</span> | ||
|- style="vertical-align: top;" | |- style="vertical-align: top; " | ||
|<span style="color: blue;">-v, --verbose</span><br/><span style="margin-left: 30px;">Increase output verbosity.</span> | |<span style="color: blue;">-v, --verbose</span><br/><span style="margin-left: 30px;">Increase output verbosity.</span> | ||
|- style="vertical-align: top; background-color: #e6e6e6;" | |- style="vertical-align: top; background-color: #e6e6e6;" | ||
|<span style="color: blue;">--version</span><br/><span style="margin-left: 30px;">Output version information and exit.</span> | |<span style="color: blue;">--version</span><br/><span style="margin-left: 30px;">Output version information and exit.</span> | ||
|- style="vertical-align: top;" | |- style="vertical-align: top; " | ||
|<span style="color: blue;">-h, --help</span><br/><span style="margin-left: 30px;">Display this help and exit.</span> | |<span style="color: blue;">-h, --help</span><br/><span style="margin-left: 30px;">Display this help and exit.</span> | ||
|} | |} | ||